Biology subjects

Ghosh, S.

Publications and source records attributed to Ghosh, S..

At least 361 records · Page 20Linked to original sources

bioRxiv2019

multiSLIDE: a query-driven heatmap visualization tool for multi-omics data

Emerging multi-omics experiments pose new challenges for exploration of quantitative data sets. We present multiSLIDE, a web-based interactive tool for simultaneous heatmap visualization of interconnected molecular features in multi-omics data sets. multiSLIDE operates by keyword search for visualizing biologically connected molecular features, such as genes in pathways and Gene Ontologies, offering convenient functionalities to rearrange, filter, and cluster data sets on a web browser in a real time basis. Various built-in querying mechanisms make it adaptable to diverse omics types, and visualizations are fully customizable. We demonstrate the versatility of the tool through three example studies, each of which showcases its applicability to a wide range of multi-omics data sets, ability to visualize the links between molecules at different granularities of measurement units, and the interface to incorporate inter-molecular relationship from external data sources into the visualization. Online and standalone versions of multiSLIDE are available at https://github.com/soumitag/multiSLIDE.

bioinformatics↗

bioRxiv2019

Insilico analysis of structural and functional impact of SNPs in Pleckstrin

Pleckstrin (PLEK) gene has been associated with a variety of disorders including autoimmune, inflammatory diseases and cancer. Mutation in this gene has been reported to be associated with autoimmune celiac disease (CD), increased atrophy in multiple sclerosis (MS), obstructive sleep apnea (OSA), abdominal aortic aneurysms, over expression in inflammatory disorders including periodontis, risk for ependymoma relapse, bladder cancer, melanoma, lung, and colorectal cancer revealing the importance of study of the PLEK. PLEK gene has been reported from other animals and therefore we have studied the molecular evolution of the PLEK gene by insilico approaches. Single nucleotide polymorphisms (SNPs), in humans have been reported to cause potential structure-function alteration in proteins. In this study we have tried to understand by insilico approaches the (i) molecular evolution of PLEK and (ii) the impact of potentially deleterious single non-synonymous SNPs (nsSNPs) on the structure and function of Pleckstrin protein. We report for the first time using molecular dynamic simulation (MDS), the impact of SNPrs17035364 and rs3816281 on the structural alterations of Pleckstrin with implications in altering its biological function which may find importance as diagnostic markers.

bioinformatics↗

bioRxiv2019

ERM-Dependent Assembly of T-Cell Receptor Signaling and Co-stimulatory Molecules on Microvilli Prior to Activation

SummaryT-cell surfaces are covered with microvilli, actin-rich and flexible protrusions. We use super-resolution microscopy to show that [≥]90% T-cell receptor (TCR) complex molecules TCR{beta} and TCR{zeta}, as well as the co-receptor CD4 and the co-stimulatory molecule CD2 reside on microvilli of human T cells. Furthermore, TCR proximal signaling molecules involved in the initial stages of the immune response, such as the protein tyrosine kinase Lck and the key adaptor molecule LAT, are also enriched on microvilli. Notably, phosphorylated proteins of the ERM (ezrin, radixin, moesin) family colocalize with these heterodimers as well as with actin filaments within the microvilli of resting T cells. This finding implies a role for one or more phosphorylated ERMs in linking the TCR complex to the actin cytoskeleton within microvilli. Indeed, expression of a dominant-negative ezrin fragment effectively redistributes TCR molecules over the whole T cell surface. Our results establish microvilli as key signaling hubs, in which the TCR complex and its proximal signaling molecules and adaptors are pre-assembled prior to activation in an ERM-dependent manner. The preformed positioning of these actin-binding TCR assemblies on individual microvilli can facilitate the local transmission of TCR signals seconds after TCR occupancy and impacts the slower subsequent events that lead to the assembly of immunological synapses.

immunology↗

bioRxiv2019

Bacterial Hyperswarming as a Protective Response to Intestinal Stress

Bacterial swarming, a collective movement on a surface, has rarely been associated with human pathophysiology. Here, we report for the first time that bacterial swarmers are associated with protection against intestinal inflammation. We show that bacterial swarmers are highly predictive of intestinal stress in mice and humans. We isolated a novel Enterobacter swarming strain, SM3, from mouse feces. SM3 and other known commensal swarmers contrast to their respective swarming-deficient, but swimming-competent isogenic strains abrogated intestinal inflammation in mice. Treatment of colitic mice with SM3, but not its mutants, enriched beneficial fecal anaerobes belonging to the family, Bacteroidales S24-7. We observed SM3 swarming associated pathways in the in vivo fecal metatranscriptomes. In vitro growth of S24-7 was enriched in presence of SM3 or its mutants conjecturing that bacterial swarming in vivo might influence SM3s access to S24-7 in the intestines. Overall, our work identifies a new paradigm in which intestinal stress allows for the emergence of swarming bacteria, which can counterintuitively heal intestinal inflammation.

microbiology↗

bioRxiv2019

Proteome-wide characterization and biomarker identification of intracranial aneurysm

The scientific basis of intracranial aneurysm (IA) formation, its rupture and further development of cerebral vasospasm remains incompletely understood. Deciphering the molecular mechanisms underlying these events will lead to identification of early detection biomarkers and in turn, improved treatment outcomes. Aberrant protein expression may drive structural alterations of vasculature found in IA. To unravel these aberrations, we performed untargeted, global, quantitative proteomic analysis of aneurysm tissue and serum from patients with IA. Samples were derived from patients of three clinical sub groups- 1) unruptured aneurysm 2) ruptured aneurysm without vasospasm 3) ruptured aneurysm who developed vasospasm. A total of 937 and 294 proteins were identified in aneurysm tissue and serum samples respectively. Several proteins that are known to maintain the structural integrity of vasculature were found to be dysregulated. ORM1, a glycoprotein, was significantly upregulated in both the aneurysm tissue and serum samples of unruptured IA patients. We employed a larger cohort of patients and validated ORM1 as a potential biomarker for screening of unruptured aneurysm using ELISA. Samples from ruptured aneurysm with vasospasm showed significant upregulation of MMP9 as compared to ruptured aneurysm without vasospasm. Using a cohort of ruptured aneurysm patients with and without vasospasm, we validated MMP9 as a potential biomarker for vasospasm. This study reveals pathophysiology underlying different clinical sub groups of IA and also suggests potential biomarkers.

neuroscience↗

bioRxiv2019

Anastrozole mediated modulation of mitochondrial activity by inhibition of mitochondrial permeability transition pore opening: An initial perspective

BackgroundMitochondrial permeability transmembrane pore [mPTP] plays a vital role in alteration of the structure and function of mitochondria. Cyclophillin D is a mitochondrial protein that regulates mPTP function and a known drug target for therapeutic studies involving mitochondria. While aromatase inhibitors role on mPTP has been previously studied, the role of anastrazole on mPTP is not completely elucidated.\n\nMethodsThe role of anastrozole in modulating the mPTP was evaluated by docking and molecular dynamics using human cyclophillin D data. Peripheral blood mononuclear cells [PBMCs] of patients with mitochondrial disorders and healthy controls were treated with anastrazole and evaluated for mean fluorescence by flow cytometer. Spectrophotometry was employed for total ATP level estimation.\n\nFindingsAnastrozole - cyclophillin D complex is more stable when compared to cyclosporine A - cyclophillin D. Anastrozole performed better than cyclosporine in inhibiting mPTP pore. Additional effects included reduction in mitochondrial swelling and mitochondrial membrane depolarization, decreased super oxide generations, caspase 3 intrinsic activity and cellular apoptosis levels and increase in ATP levels.\n\nInterpretationThese results highlights the potency of anastrozole as a promising agent in ameliorating the phenotype by inhibiting the opening of mPTP pore. However, larger functional studies are required to validate the efficacy of this molecule as a therapeutic agent in mitochondrial disorders.

molecular biology↗

bioRxiv2019

Machine Learning for Prioritization of Thermostabilizing Mutations for G-protein Coupled Receptors

Although the three-dimensional structures of G-protein-coupled receptors (GPCRs), the largest superfamily of drug targets, have enabled structure-based drug design, there are no structures available for 87% of GPCRs. This is due to the stiff challenge in purifying the inherently flexible GPCRs. Identifying thermostabilized mutant GPCRs via systematic alanine scanning mutations has been a successful strategy in stabilizing GPCRs, but it remains a daunting task for each GPCR. We developed a computational method that combines sequence, structure and dynamics based molecular properties of GPCRs that recapitulate GPCR stability, with four different machine learning methods to predict thermostable mutations ahead of experiments. This method has been trained on thermostability data for 1231 mutants, the largest publicly available dataset. A blind prediction for thermostable mutations of the Complement factor C5a Receptor retrieved 36% of the thermostable mutants in the top 50 prioritized mutants compared to 3% in the first 50 attempts using systematic alanine scanning.\n\nStatement Of SignifiganceG-protein-coupled receptors (GPCRs), the largest superfamily of membrane proteins play a vital role in cellular physiology and are targets to blockbuster drugs. Hence it is imperative to solve the three dimensional structures of GPCRs in various conformational states with different types of ligands bound. To reduce the experimental burden in identifying thermostable GPCR mutants, we report a computational framework using machine learning algorithms trained on thermostability data for 1231 mutants and features calculated from analysis of GPCR sequences, structure and dynamics to predict thermostable mutations ahead of experiments. This work represents a significant advancement in the development, validation and testing of a computational framework that can be extended to other class A GPCRs and helical membrane proteins.

biophysics↗

bioRxiv2019

Pathognomonic and epistatic genetic alterations in B-cell non-Hodgkin lymphoma

B-cell non-Hodgkins lymphoma (B-NHL) encompasses multiple clinically and phenotypically distinct subtypes of malignancy with unique molecular etiologies. Common subtypes of B-NHL such as diffuse large B-cell lymphoma (DLBCL) have been comprehensively interrogated at the genomic level. But rarer subtypes such as mantle cell lymphoma (MCL) remain sparsely characterized. Furthermore, multiple B-NHL subtypes have thus far not been comprehensively compared using the same methodology to identify conserved or subtype-specific patterns of genomic alterations. Here, we employed a large targeted hybrid-capture sequencing approach encompassing 380 genes to interrogate the genomic landscapes of 685 B-NHL tumors at high depth; including DLBCL, MCL, follicular lymphoma (FL), and Burkitt lymphoma (BL). We identified conserved hallmarks of B-NHL that were deregulated in the majority of tumor from each subtype, including the frequent genetic deregulation of the ubiquitin proteasome system (UPS). In addition, we identified subtype-specific patterns of genetic alterations, including clusters of co-occurring mutations and DNA copy number alterations. The cumulative burden of mutations within a single cluster were more discriminatory of B-NHL subtypes than individual mutations, implicating likely patterns of genetic cooperation that contribute to disease etiology. We therefore provide the first cross-sectional analysis of mutations and DNA copy number alterations across major B-NHL subtypes and a framework of co-occurring genetic alterations that deregulate genetic hallmarks and likely cooperate in lymphomagenesis.

genomics↗

bioRxiv2019

Copulas reveal complex and informative dependencies propagating throughout ecology

All branches of ecology study relationships among and between environmental and biological variables. However, standard approaches to studying such relationships, based on correlation and regression, provide only a small slice of the complex information contained in the relationships. Other statistical approaches exist that provide a complete description of relationships between variables, based on the concept of the copula; they are applied in finance, neuroscience and other fields, but rarely in ecology. We here explore the concepts that underpin copulas and examine the potential for those concepts to improve our understanding of ecology. We find that informative copula structure in dependencies between variables is common across all the environmental, species-trait, phenological, population, community, and ecosystem functioning datasets we considered. Many datasets exhibited asymmetric tail associations, whereby two variables were more strongly related in their left compared to right tails, or vice versa. We describe mechanisms by which observed copula structure and asymmetric tail associations can arise in ecological data, including a Moran-like effect whereby dependence structures between environmental variables are inherited by ecological variables; and asymmetric or nonlinear influences of environments on ecological variables, such as under Liebigs law of the minimum. We also describe consequences of copula structure for ecological phenomena, including impacts on extinction risk, Taylors law, and the stability through time of ecosystem services. By documenting the importance of a complete description of dependence between variables, advancing conceptual frameworks, and demonstrating a powerful approach, we aim to encourage widespread use of copulas in ecology, which we believe can benefit the discipline.

ecology↗

bioRxiv2019

Aggregation dynamics of charged peptides in water: effect of salt concentration

Extensive molecular dynamics simulations have been employed to probe the effects of salts on the kinetics and dynamics of early-stage aggregated structures of steric zipper peptides in water. The simulations reveal that the chemical identity and valency of cation in the salt play a crucial roles in aggregate morphology of the peptides. Sodium ions induce the most aggregated structures but this is not replicated by potassium ions which are also monovalent. Divalent Magnesium ions induce aggregation, but to a lesser extent than that of sodium and their interactions with the charged peptides are also significantly different. The aggregate morphology in the presence of monovalent sodium ions is a compact structure with interpenetrating peptides, which differs from the more loosely connected peptides in the presence of either potassium or magnesium ions. The different ways in which the cations effectively renormalize the charges of peptides is suggested to be the cause of the differential effects of different salts studied here. These simulations underscore the importance of understanding both the valency and nature of of salts in biologically relevant aggregated structures.

biophysics↗

bioRxiv2019

Motility of Enzyme-Powered Vesicles

Autonomous nanovehicles powered by energy derived from chemical catalysis have potential applications as active delivery agents. For in vivo applications, it is necessary that the engine and its fuel, as well as the chassis itself, be biocompatible. Enzyme molecules have been shown to generate mechanical force through substrate turnover and are attractive candidates as engines; phospholipid vesicles are biocompatible and can serve as cargo containers. Herein, we describe the autonomous movement of vesicles with membrane-bound enzymes in the presence of the substrate. We find that the motility of the vesicles increases with increasing enzymatic turnover rate. The enhanced diffusion of these enzyme-powered systems was further substantiated in real time by tracking the motion of the vesicles using optical microscopy. The membrane-bound protocells that move by transducing chemical energy into mechanical motion serve as models for motile living cells and are key to the elucidation of the fundamental mechanisms governing active membrane dynamics and cellular movement.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC=\"FIGDIR/small/645986v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (30K):\norg.highwire.dtl.DTLVardef@49a48org.highwire.dtl.DTLVardef@2d0bc0org.highwire.dtl.DTLVardef@15e9466org.highwire.dtl.DTLVardef@60ba5e_HPS_FORMAT_FIGEXP M_FIG \"For Table of Contents Only\"\n\nC_FIG

biochemistry↗

bioRxiv2019

Investigating Coronary Artery Disease methylome through targeted bisulfite sequencing

BackgroundGene environment interactions leading to epigenetic alterations play pivotal role in the pathogenesis of Coronary Artery Disease (CAD). Altered DNA methylation is one such epigenetic factor that could lead to altered disease etiology. In this study, we comprehensively identified methylation sites in several genes that have been previously associated with young CAD patients.\n\nMethodsThe study population consisted of 42 healthy controls and 33 young CAD patients (age group < 50 years). We performed targeted bisulfite sequencing of promoter as well as genic regions of several genes in various pathways like cholesterol synthesis and metabolism, endothelial dysfunction, apoptosis, which are implicated in the development of CAD.\n\nResultsWe observed that the genes like GALNT2, HMGCR were hypermethylated in the promoter whereas LDLR gene promoter was hypomethylated indicating that intracellular LDL uptake was higher in CAD patients. Although APOA1 did not show significant change in methylation but APOC3 and APOA5 showed variation in methylation in promoter and exonic regions. Glucokinase (GCK) and endothelial nitric oxide synthase 3 (NOS3) were hyper methylated in the promoter. Genes involved in apoptosis (BAX/BCL2/AKT2) and inflammation (PHACTR1/LCK) also showed differential methylation between controls and CAD patients.\n\nConclusionsThis study is unique because it highlights important gene methylation alterations which might predict the risk of young CAD in Indian population. Large scale studies in different populations would be important for validating our findings and understanding the epigenetic events associated with CAD.

genomics↗

bioRxiv2019

AGO1x prevents dsRNA-induced interferon signaling to promote breast cancer cell proliferation

Initially reported for viral RNA, elongation of polypeptide chains beyond the stop codon (translational readthrough (TR)) also occurs on eukaryotic transcripts. TR diversifies the proteome and can modulate protein levels 1-6. Here we report that AGO1x, a conserved TR isoform of Argonaute 1, is generated in highly proliferative breast cancer cells, where it curbs accumulation of double stranded RNAs, the induction of the interferon response and apoptosis. In contrast to other mammalian Argonaute protein family members with primarily cytoplasmic functions, AGO1x localizes to the nucleus, in the vicinity of nucleoli. We identify a novel interaction of AGO1x with the Polyribonucleotide Nucleotidyltransferase 1, depletion of either protein leading to dsRNA accumulation and impaired cell proliferation. Our study thus uncovers a novel function of an Argonaute protein outside of the miRNA effector pathway, in buffering dsRNA-induced interferon responses. As AGO1x expression is tightly linked to breast cancer cell proliferation, our study suggests a new direction for limiting tumor growth.

cell biology↗

bioRxiv2019

Divergence from conserved residues underlies intracellular retention of mammalian odorant receptors

Mammalian odorant receptors are a diverse and rapidly evolving set of G protein-coupled receptors expressed in olfactory cilia membranes. Most odorant receptors show little to no cell surface expression in non-olfactory cells due to endoplasmic reticulum retention, which has slowed down biochemical studies. Here, we provide evidence that structural instability and divergence from conserved residues of individual odorant receptors underlie intracellular retention using a combination of large-scale screening of odorant receptors cell surface expression in heterologous cells, point mutations, structural modeling, and machine learning techniques. We demonstrate the importance of conserved residues by synthesizing "consensus" odorant receptors that show high levels of cell surface expression similar to conventional G protein-coupled receptors. Furthermore, we associate in silico structural instability with poor cell surface expression using molecular dynamics simulations. We propose an enhanced evolutionary capacitance of olfactory sensory neurons that enable the functional expression of odorant receptors with cryptic mutations. Significance StatementOdor detection in mammals depends on the largest family of G protein-coupled receptors, the odorant receptors, which represent [~]2% of our protein-coding genes. The vast majority of odorant receptors are trapped within the cell when expressed in non-olfactory cells. The underlying causes of why odorant receptors cannot be functionally expressed in non-olfactory cells have remained enigmatic for over 20 years. Our study points to divergence from a consensus sequence as a key factor in a receptors inability to function in non-olfactory cells, which in turn, helps explain odorant receptors exceptional functional diversity and rapid evolution. We also show the success of protein engineering strategies for promoting odorant receptor cell surface expression.

cell biology↗

bioRxiv2019

Non-uniform Crowding Enhances Transport: Relevance to Biological Environments

The cellular cytoplasm is crowded with macromolecules and other species that occupy up to 40% of the available volume. Previous studies have reported that for high crowder molecule concentrations, colloidal tracer particles have a dampened diffusion due to the higher solution viscosity. However, these studies employed uniform distributions of crowder molecules. We report a scenario, previously unexplored experimentally, of increased tracer transport driven by a non-uniform concentration of crowder macromolecules. In gradients of polymeric crowder, tracer particles undergo transport several times higher than that of their bulk diffusion rate. The direction of the transport is toward regions of lower crowder concentration. Mechanistically, hard-sphere interactions and the resulting volume exclusion between the tracer and crowder increases the effective diffusion by inducing a convective motion of tracers. Strikingly, soft deformable particles show even greater enhancement in transport in crowder gradients compared to similarly sized hard particles. We propose a model that supports the data and quantifies a \"diffusiophoretic buoyancy force\" when a tracer is in a gradient of crowder concentration. Overall, this demonstration of enhanced transport in non-uniform distributions of crowder is anticipated to clarify aspects of multi-component intracellular transport.

biophysics↗

bioRxiv2019

Visual area V4 encodes history dependent attentional effort and single-trial perceptual detection

Understanding how activity of visual neurons represents distinct components of attention and their dynamics that account for improved visual performance remains elusive because single-unit experiments have not isolated the intensive aspect of attention from attentional selectivity. We isolated attentional intensity and its single trial dynamics as determined by spatially non-selective attentional performance in an orientation discrimination task while recording from neurons in monkey visual area V4. We found that attentional intensity is a distinct cognitive signal that can be distinguished from spatial selectivity, reward expectations and motor actions. V4 spiking on single trials encodes a combination of sensory and cognitive signals on different time scales. Attentional intensity and the detection of behaviorally relevant sensory signals are well represented, but immediate reward expectation and behavioral choices are poorly represented in V4 spiking. These results provide a detailed representation of perceptual and cognitive signals in V4 that are crucial for attentional performance.

neuroscience↗

bioRxiv2019

Extracellular Caspase-1 regulates migration of hair follicle stem cells upon wounding

The wound-healing process is a paradigm of the directed migration of various pools of stem cells from their niche to the site of injury where they replenish damaged cells. Two decades have elapsed since the observation that wounding activates multipotent hair follicle stem cells to infiltrate the epidermis, but the cues that coax these cells out of their niche remains unknown. Using an excisional wound and genetic mouse models of wound healing, we discovered that Caspase-1, a protein classically known as an integral component of the cytosolic inflammasome, is secreted and has a non-canonical role in the extracellular milieu. Through its Caspase Activation Recruitment Domain (CARD), Caspase-1 is sufficient to initiate chemotaxis of hair follicle stem cells into the epidermis. Uncovering this novel function of Caspase-1 also facilitates a deeper understanding of the mechanistic basis of the epithelial hyperplasia found to accompany numerous inflammatory skin diseases.

cell biology↗

bioRxiv2018

In vivo generation of post-infarct mouse cardiac muscle by cardiomyocyte progenitors produced with a reproducible laminin-promoted human stem cell differentiation system

Regeneration of human heart muscle after injury is extremely limited and an unmet clinical need. Despite extensive research, there are no methods for the reproducible generation of clinical quality stem-cell-derived cardiovascular progenitors (CVPs). Here, we identified laminin-221 (LN-221) as the main cardiac laminin, which was produced here as human recombinant protein, and showed that LN-221 promotes differentiation of pluripotent hESCs towards cardiomyocyte lineage and downregulates genes associated with pluripotency and teratoma development. We developed a chemically defined, xeno-free laminin-based cardiomyocyte differentiation protocol to reproducibly generate CVPs that form human muscle in vivo. We assessed the reproducibility of the differentiation protocol using time-course bulk RNA sequencing developed from two different hESC lines. Single-cell RNA sequencing of CVPs derived from two hESC lines further showed high reproducibility and identified three main progenitor subpopulations. These CVPs were transplanted into myocardial infarction mice, where heart function was measured by echocardiogram and human heart muscle bundle formation was identified histologically. This method may provide clinical quality cells for use in regenerative cardiology.

cell biology↗